November 9, 2012 12:42am ESTNovember 8, 2012 2:01pm ESTSan Jose and Kansas City are out of the MLS Cup playoffs, despite being the best teams in their conference. Why? Because their flaws are exposed in a short series by veteran playoff clubs, Brian Straus says.

Wednesday's postseason carnage appeared surprising, even by the chaotic and unpredictable standards of the MLS Cup playoffs.

For just the second time in the league's 17-year history, the top two seeds were ousted in the quarterfinals.

The Supporters Shield-winning San Jose Earthquakes—well-rested and powered by the most productive offense the league had seen since the late 1990s—were knocked out by the rival Los Angeles Galaxy 3-2 on aggregate following Wednesday's 3-1 loss.

Sporting Kansas City finished atop the Eastern Conference thanks largely to a defense that was the third-best in league annals. After tasting defeat in last year's semifinal and winning the 2012 U.S. Open Cup, the club appeared poised to take the next step. But Wednesday's 1-0 win over the visiting Houston Dynamo wasn't enough. SKC was eliminated 2-1 on aggregate.

Under pressure to make the regular season more meaningful, MLS last year added a fifth playoff qualifier and a one-game preliminary round in each conference. It hadn't been uncommon for at least one top seed to fall at the first hurdle. The extra game was installed in part to offer the two favorites a boost by pitting them against tired opposition in the quarterfinals. It worked like a charm in 2011—SKC and L.A. swept the preliminary-round survivors out of the playoffs.

This year, in addition to overcoming the burden of an extra playoff game, Houston and L.A. spent the fall negotiating the group stage of the CONCACAF Champions League. Their MLS Cup quarterfinal opponents were better rested and on a roll. Sporting hadn't lost since late July. The Earthquakes hadn't been beaten since the middle of August.

But there were other factors working against the favorites—fatal flaws that weren't exposed over the course of a long regular season but which were exploited in a short playoff series by experienced and talented playoff opposition.

Both San Jose and Sporting K.C. had been pressing its luck for months.

The Earthquakes had been falling behind and scoring late goals—including an astonishing nine in second-half stoppage time—thanks to their "Goonies Never Say Die" ethos and a direct, long-ball attack well suited to creating chaos in the waning seconds and anchored by the unique skills of forwards Chris Wondolowski (27 regular-season goals), Steven Lenhart (10) and Alan Gordon (13).

Meanwhile, Sporting couldn't score. Their 42 regular-season goals ranked ninth out of 10 playoff teams (below only 11-13-10 Vancouver) and 13th overall. The club's leading scorer, Kei Kamara (11 goals), was expected to fill a playmaking role as well as a wide forward in coach Peter Vermes' 4-3-3. That's a lot to place on one man's shoulders, and with Teal Bunbury injured and C.J. Sapong in his second season, it was easy to imagine SKC dominating a game but simply failing to find the finishing needed to advance.

It also was easy to imagine San Jose digging a hole it couldn't escape.

That's what happened Wednesday.

Landon Donovan and Robbie Keane ran rampant and saw to it that San Jose, absent injured central defender Victor Bernárdez and with a bit of reshuffling required as a result, had to score twice in the second half to force overtime. The Earthquakes recovered from two-goal deficits twice before against L.A., but that's hardly a recipe for long-term success.

Gordon scored in the 82nd minute to pull San Jose to within one on aggregate, but that's where the season ended.

"I wouldn't say that it is luck," Earthquakes coach Frank Yallop said of the frequent comebacks. "We have had some great battles against L.A. The story has been us going down and then coming back, but that is what we do. We keep going. I think that to go three (goals) down is a big mountain to climb. If it had just been two down, we would have equalized."

Trailing 2-0 after the first leg, SKC dominated Houston at Livestrong Sporting Park on Wednesday.

"I think it was, in the three years that I've been coaching the team, the best performance we had in 90 minutes. We absolutely dominated the game. Guys played with incredible, incredible concentration and organization," Vermes told reporters. "I thought it was just a complete game, other than getting a second goal, we created some very good chances."

Despite controlling a Barcelona-like 71 percent of the possession and attempting 20 shots, SKC got one goal. It came on a diving header from defender Seth Sinovic in the 64th minute—it was the third-year pro's first MLS goal.

Sapong had a golden opportunity in the 73rd but lifted his shot over the crossbar after running onto a beautiful pass from Kamara.

"We always got the results we needed," Sapong said via the league's website. "Because of our stingy defense, we were never in a position where we had to score so many goals. It definitely is a concern when the ball doesn't roll your way so many times, but at this point all we can do is train hard in the offseason and try to make a run again next year."

Both San Jose and SKC were excellent teams—that was proven over the 34-game regular season. But both had obvious flaws that spelled doom in the playoffs, where the margin for error is so much slimmer. It was a perfect storm for both. Bernárdez's injury and L.A.'s talent produced a deficit that San Jose couldn't overhaul. Houston's savvy and opportunism in the first leg—part of the postseason foundation built by coach Dom Kinnear—was going to test Kansas City's offensive resilience and creativity in Wednesday's decider.

So much for extra rest and momentum. The road to the MLS Cup title rewards balance and often punishes teams that roll the dice once too often. This year's top seeds learned that harsh lesson Wednesday night.